Contacts of the helix formed by residues 286 - 305 (chain B) in PDB entry 1NUA
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 286 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B ARG* 3.7 38.6 - - + +
187B GLU* 3.4 24.2 - - - +
190B ASN* 3.3 28.3 - - + +
278B GLU* 4.1 1.6 - - - -
283B PRO 4.5 11.9 - - - +
284B GLN 4.9 0.4 - - - +
285B ILE* 1.3 77.4 - - - +
287B HIS* 1.3 66.5 + - - +
288B GLY 3.4 0.2 - - - -
289B GLU* 2.8 21.1 + - - +
290B CYS* 3.0 22.4 + - - -
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Residues in contact with HIS 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LEU* 4.5 23.3 - - + -
190B ASN* 4.7 1.7 - - - +
194B GLU* 2.8 11.2 + - - -
271B HIS* 3.3 10.0 + + - -
275B HIS* 3.8 13.2 - + - -
278B GLU* 3.1 36.6 + - - +
286B LEU* 1.3 71.9 - - - +
288B GLY* 1.3 61.2 + - - +
290B CYS* 3.1 3.3 + - - +
291B VAL* 2.8 52.3 + - + +
601B ZN 2.1 36.9 - - - -
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Residues in contact with GLY 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LEU* 5.5 1.1 - - - +
190B ASN* 2.9 36.0 + - - +
193B ALA* 3.2 21.3 - - - +
194B GLU* 5.6 2.9 - - - -
287B HIS* 1.3 80.9 - - - +
289B GLU* 1.3 56.9 + - - +
291B VAL* 3.5 3.5 + - - -
292B ALA* 2.9 25.1 + - - +
325B LEU* 4.0 2.4 - - - +
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Residues in contact with GLU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ARG* 2.6 53.3 + - - +
189B ILE* 5.8 2.9 - - + +
190B ASN* 3.6 13.9 - - + +
285B ILE* 3.3 15.7 - - + +
286B LEU* 2.8 26.7 + - + +
288B GLY* 1.3 75.6 - - - +
290B CYS* 1.3 63.8 + - - +
292B ALA* 3.2 16.8 + - - +
293B ILE* 3.3 13.3 - - - +
325B LEU* 4.1 12.8 - - + -
326B PRO* 3.6 22.1 - - + +
333B ARG* 5.9 0.7 + - - -
334B ILE* 5.1 5.9 - - - +
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Residues in contact with CYS 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B GLY* 3.7 22.3 - - - +
277B ILE* 3.9 15.3 - - + +
278B GLU* 3.4 36.6 - - + +
281B LEU* 4.6 1.8 - - - -
285B ILE* 3.8 23.6 - - - -
286B LEU 3.0 17.0 + - - +
287B HIS 3.6 5.6 - - - +
289B GLU* 1.3 78.3 - - - +
291B VAL* 1.3 51.8 + - + +
293B ILE* 3.1 11.2 + - - +
294B GLY* 2.7 31.5 + - - -
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Residues in contact with VAL 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ALA* 4.9 2.9 - - + +
194B GLU* 4.5 7.9 - - - +
197B LYS* 4.9 1.8 - - + -
269B TRP 4.5 1.3 - - - +
270B GLY 4.1 6.7 - - - +
271B HIS* 3.6 36.8 - - + +
274B GLY* 4.3 6.7 - - - -
275B HIS* 5.3 0.2 - - + -
278B GLU* 6.5 0.2 - - + -
287B HIS* 2.8 54.5 + - + +
288B GLY* 3.9 7.0 - - - +
290B CYS* 1.3 72.3 - - + +
292B ALA* 1.3 57.6 + - - +
294B GLY 4.2 1.1 - - - +
295B MET* 2.8 46.5 + - + +
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B GLY 2.9 13.8 + - - +
289B GLU* 3.2 12.3 - - - +
290B CYS 3.1 0.2 - - - -
291B VAL* 1.3 74.0 - - - +
293B ILE* 1.3 64.9 + - - +
295B MET* 3.2 14.7 + - - +
296B VAL* 3.1 27.9 + - - +
320B LEU* 3.5 8.3 - - + +
325B LEU* 4.0 25.6 - - + -
326B PRO 3.3 18.4 - - - +
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Residues in contact with ILE 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ILE* 5.0 6.5 - - + -
289B GLU 3.3 12.3 - - - +
290B CYS* 3.1 9.4 + - - +
292B ALA* 1.3 74.8 - - - +
294B GLY* 1.3 58.5 + - - +
296B VAL* 3.3 9.3 + - + +
297B LYS* 3.0 43.1 + - + +
326B PRO* 3.4 33.7 - - + +
327B THR 4.1 2.0 - - - +
328B SER* 3.2 44.6 - - - +
329B LEU* 4.0 26.9 - - + +
334B ILE* 5.1 4.7 - - + -
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Residues in contact with GLY 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B GLY 3.3 23.3 - - - -
273B ILE* 4.3 8.5 - - - +
274B GLY* 3.8 10.5 - - - -
277B ILE* 5.2 0.6 - - - +
290B CYS 2.7 13.8 + - - -
291B VAL 3.6 1.1 - - - -
292B ALA 3.1 0.2 - - - -
293B ILE* 1.3 75.1 - - - +
295B MET* 1.3 58.7 + - - +
297B LYS* 3.3 3.2 + - - +
298B GLU* 2.8 34.3 + - - +
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Residues in contact with MET 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ALA* 3.4 21.3 - - + +
196B ILE* 4.9 1.8 - - - -
197B LYS* 3.8 22.2 - - - -
269B TRP* 3.4 46.5 - - + +
270B GLY* 3.5 18.1 - - - -
291B VAL* 2.8 31.8 + - + +
292B ALA* 3.2 11.2 + - - +
294B GLY* 1.3 70.0 - - - +
296B VAL* 1.3 60.8 + - - +
298B GLU* 3.3 0.9 + - - -
299B ALA* 2.8 33.7 + - - +
316B ILE* 4.6 1.1 - - - -
320B LEU* 3.5 34.3 - - + -
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Residues in contact with VAL 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ALA 3.1 17.3 - - - +
293B ILE* 3.3 7.6 - - + +
295B MET* 1.3 76.5 - - - +
297B LYS* 1.3 65.3 - - + +
299B ALA* 3.0 9.7 + - - +
300B GLU* 2.9 41.0 + - + +
313B VAL* 4.8 0.5 - - - +
316B ILE* 4.5 4.5 - - + -
317B VAL* 3.9 25.1 - - + -
320B LEU* 3.5 19.5 - - + -
327B THR* 3.6 35.0 - - - +
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Residues in contact with LYS 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ILE* 3.4 35.3 - - + +
277B ILE* 5.4 2.7 - - + +
293B ILE* 3.0 33.7 + - + +
294B GLY 3.6 5.6 - - - +
296B VAL* 1.3 77.7 - - + +
298B GLU* 1.3 57.4 + - - +
300B GLU* 2.9 35.4 + - - +
301B LEU* 2.9 13.5 + - - +
327B THR 5.7 0.4 + - - -
328B SER* 5.4 2.8 - - - +
329B LEU* 4.4 21.0 - - - +
348B LEU* 6.6 0.2 - - - -
390B VAL* 3.1 33.5 - - + +
391B LEU* 4.5 11.0 - - + +
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Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B ASN 3.9 1.4 - - - +
269B TRP* 3.6 18.7 + - + +
270B GLY* 2.6 31.5 + - - +
272B SER* 2.8 28.2 + - - -
273B ILE* 2.9 25.8 + - + -
294B GLY 2.8 17.9 + - - +
295B MET 3.6 3.6 - - - +
297B LYS* 1.3 72.3 - - - +
299B ALA* 1.3 59.6 + - - +
301B LEU* 3.8 9.1 - - + +
302B ALA* 3.5 15.1 + - - +
365B ILE* 3.1 33.6 - - + +
366B VAL 3.7 8.3 + - - +
367B LEU* 4.0 10.2 - - - +
368B LEU 5.5 0.2 + - - -
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Residues in contact with ALA 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B TRP* 4.1 15.9 - - + +
295B MET 2.8 19.0 + - - +
296B VAL* 3.3 7.4 - - - +
297B LYS 3.0 0.2 - - - -
298B GLU* 1.3 75.4 - - - +
300B GLU* 1.3 65.4 + - - +
301B LEU 3.2 0.2 - - - -
302B ALA* 3.4 1.9 + - - +
303B ARG 3.2 15.6 + - - -
308B LEU* 3.3 29.7 - - + +
313B VAL* 3.6 14.3 - - + +
316B ILE* 4.6 11.0 - - + -
368B LEU* 6.4 1.3 - - - -
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Residues in contact with GLU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B VAL* 2.9 28.1 + - + +
297B LYS* 2.9 31.4 + - - +
299B ALA* 1.3 78.0 - - - +
301B LEU* 1.3 50.6 + - - +
303B ARG* 3.0 17.8 + - - +
304B HIS* 2.8 33.4 + - - +
313B VAL* 4.3 15.5 - - + -
390B VAL* 4.1 17.7 - - + +
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Residues in contact with LEU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ILE* 5.3 3.1 - - + -
297B LYS 2.9 13.7 + - - +
298B GLU* 3.8 8.7 - - - +
299B ALA 3.2 0.2 - - - -
300B GLU* 1.3 74.6 - - - +
302B ALA* 1.3 66.5 + - - +
304B HIS* 3.0 15.4 + - + +
305B LEU* 2.9 30.7 + - + +
365B ILE* 4.1 28.7 - - + -
367B LEU* 4.5 5.8 - - + -
382B VAL* 4.1 16.4 - - + -
386B ASP* 3.3 33.2 - - + +
387B ILE* 4.0 24.7 - - + +
390B VAL* 4.0 15.2 - - + +
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Residues in contact with ALA 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B GLU 3.5 10.4 + - - +
299B ALA* 3.4 6.4 + - - +
300B GLU 3.3 0.6 - - - -
301B LEU* 1.3 78.0 - - - +
303B ARG* 1.3 57.0 + - - +
305B LEU* 3.4 1.2 + - - -
306B GLY 3.3 2.3 + - - -
307B ILE* 2.7 42.4 + - + +
308B LEU* 2.8 13.6 + - + +
367B LEU* 4.0 18.1 - - + +
368B LEU 3.3 29.4 - - - +
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Residues in contact with ARG 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B ALA 3.2 11.6 + - - +
300B GLU* 3.0 19.2 + - - +
302B ALA* 1.3 78.3 - - - +
304B HIS* 1.3 56.8 + - - +
306B GLY* 3.0 18.0 + - - -
308B LEU* 3.1 21.1 - - - +
310B GLY* 3.1 31.8 - - - +
313B VAL* 4.0 18.4 - - + -
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Residues in contact with HIS 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B GLU 2.8 12.9 + - - +
301B LEU* 3.0 15.2 + - + +
303B ARG* 1.3 74.9 - - - +
305B LEU* 1.3 72.8 + - + +
306B GLY 3.1 5.9 + - - -
386B ASP* 2.7 42.5 + - + -
389B VAL* 3.3 28.7 - - + +
390B VAL* 4.5 4.7 - - + +
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Residues in contact with LEU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B LEU* 2.9 21.8 + - + +
303B ARG 3.3 0.2 - - - -
304B HIS* 1.3 93.7 - - + +
306B GLY* 1.3 58.6 + - - +
307B ILE* 3.1 24.4 + - + +
367B LEU* 3.3 33.4 - - + -
382B VAL* 4.0 18.6 - - + -
386B ASP* 3.9 23.1 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il